In their recent book A Scientist’s Guide to Talking with the Media (which I enthusiastically recommend, by the way), Hayes and Grossman describe the role that university press offices have in disseminating new findings by researchers at their institutions. I agree that this is an important job and that good press releases can have a very positive effect. The corollary, of course, would be that poorly crafted ones can sow confusion. I have been critical of science blogs and science news services in the past, but in some cases they are simply re-posting (albeit uncritically) the stories from press offices, which may be where the actual problem is.
Witness two frustrating examples from genome biology. The first was by the press office at Johns Hopkins [How Neutral Genetic Drift Shaped Our Genome], and was re-posted by some science blogs. The second is by the University of California, San Diego, and is re-posted at ScienceDaily and Scientific Blogging [One Man’s Junk May Be A Genomic Treasure].
Both stories are guilty of over-hyping the significance of the research (which perhaps is not surprising) and of including significant factual errors (which is not acceptable). Notably, the Johns Hopkins release mangles basic evolutionary theory, and now we have this from UC San Diego:
Scientists have only recently begun to speculate that what’s referred to as “junk” DNA — the 96 percent of the human genome that doesn’t encode for proteins and previously seemed to have no useful purpose — is present in the genome for an important reason. But it wasn’t clear what the reason was. Now, researchers at the University of California, San Diego (UCSD) School of Medicine have discovered one important function of so-called junk DNA.
The first line is patently false. In my area of study, I encounter far toomany speculations regarding functions for non-coding DNA, and this is how the situation has been for decades. It also bears noting that the study in question studied one transposable element, SINE B2, which makes up around 2.4% of the mouse genome and appears to contribute to the regulation of a growth hormone gene. This is not very surprising; recall that McClintock first characterized transposable elements as “controlling elements”, and even the earliest and most vocal proponents of the “selfish DNA” hypothesis surmised that some TEs would have regulatory functions. SINE B2 itself has been implicated in regulation at least since 1984 (see also here from 2001). This is not in any way a critical comment about the work — it is sure to be an interesting study and I look forward to reading the article when it appears in Science this week. But this press release — which I suspect had little to do with the authors of the study — is vastly overstated to the point of twisting the history of the discipline. (They also suggest that protein-coding genes make up 4% of the human genome whereas the real total is less than 2%, but that’s a comparatively minor issue).
I am very interested in working with the media to provide accessible, interesting, and (not or) accurate information to the public. I also realize that writing about scientific research is difficult, and that there are many individuals out there who areverygood at it. I don’t like to be critical all the time, but we really must clean up reports on “junk DNA”. I am open to any suggestions on how scientists can help to make this a reality.
More later, but just a quick post to give credit where it is due. Kudos to New Scientist for their excellent story “Why ‘junk DNA’ may be useful after all” in the July 14 issue. Aria Pearson gets the complexity of the situation right while making the piece interesting and accessible.
As an update to the previous post about the acceptance of evolution in Canada vs. the USA, here are some highlights from a recently published (July 3) poll by Canadian Press-Decima Research. This is useful because it breaks the issue down into young earth creationism, theistic evolution, and naturalistic evolution in the way that American polls have in some cases.
Less than one in three Canadians (29%) believe that God had no part in the creation or development of human beings.
Fewer still (26%) believe “that God created human beings pretty much in their present form at one time within the last 10,000 years or soâ€.
A plurality, but still only 34%, say that “human beings have developed over millions of years from less advanced forms of life, but God guided this processâ€.
Belief in creationism is lowest in Quebec (21%), Alberta (22%), and B.C. (22%). In Alberta, the plurality view is that God guided human development (39%), while in Quebec the plurality feels God played no part (40%).
Rural residents are 12 points more likely than urban dwellers to believe that God created humans in their present form. Differences by generation are not all that large. The plurality of women (37%) believes that God guided the process, while the plurality of men (35%) believes that God played no part.
In polls using the same question (Gallup) put to US residents, findings are different: 45% said God created humans in more or less their present form (compared to 26% in Canada), 40% said that God guided the evolutionary process (compared to 34% in Canada). Only 15% say God played no part (compared to 29% in Canada).
According to Decima CEO Bruce Anderson “These results reflect an essential Canadian tendency: we are pretty secular, but pretty hesitant to embrace atheism. Our views on the role of science and spirituality lack consensus but these are not polarizing issues for the most part. It’s more as though for many, these feelings are unresolved, we believe in a higher being, we know what we don’t know, are comfortable not knowing, and choose not to press our views upon one another.â€
Intelligent design proponents claim to base their views entirely on scientific data, and argue that the design perspective is more productive than an evolutionary approach. One area where this is particularly evident is in discussions of “junk DNA”. Indeed, with every new discovery (by evolutionary biologists) that some part of the genome shows signs of function, ID proponents suggest that it is they, and not evolutionary biologists, who predicted from the outset that non-coding DNA would prove to be functional. I won’t repeat the discussion of why it is incorrect to suggest that most biologists have stubbornly refused to consider functions for non-coding DNA (see here and here). Instead, what I want to do is to give ID proponents an opportunity to show that their perspective really is scientific and that it can lead to a better description and explanation for biological phenomena than evolutionary science can.
Here is what ID proponents need to do:
1) Specify the basis for assuming that all non-coding DNA must be functional. This makes implicit assumptions about the designer and the design process (namely, that he/she/it would not produce non-functional features of organisms). This assumption must be justified. It also opens the discussion to more philosophical questions, such as why the designer would choose to design such a massive number of pathogens and parasites. Either one can know the designer’s plan or one cannot; if the former, then the way that one would come to know this must be explicated.
2) Specify how one would go about demonstrating evidence of functions for non-coding DNA in the absence of a framework based on common descent. To date, most evidence for function comes from demonstrations of conservation of non-coding sequences, which indicates that constraints imposed by natural selection have maintained these sequences over long spans of evolutionary time. ID would need to propose a testable means of identifying functional sequences that does not rely on the assumption of common descent. Also, it should be recalled that, at present, there is suggestive evidence that about 5% of the human genome is functional. It will be necessary to specify how function will be demonstrated in the other 95% of the genome.
3) Make specific predictions about what function(s) all non-coding DNA is likely to be fulfilling, and propose ways to test those predictions. A vague prediction that all non-coding DNA will prove to be functional is not useful. Moreover, strict Darwinian theory in which natural selection is assumed to remove any non-functional features makes exactly the same prediction, so this does not distinguish ID from Darwinian theory.
4) Propose functions for transposable elements that take into account their parasitic characteristics (e.g., as disease-causing mutagens) but do not invoke the notion of co-option. There are clear examples of transposable elements (TEs) that are functional, for example as regulatory sequences, in the vertebrate immune system, and in cellular stress response. However, this represents a very small percentage of TEs, most of which are neutral or deleterious in the genome. The evolutionary explanation is that, in some relatively rare cases, these former parasites have become integrated into the functional system of the genome. This process of co-option of function is the same process that evolutionary biologists use in explanations of the evolution of complex structures such as eyes or flagella. If co-option is ruled out a priori, then it cannot be used to explain the acquisition of function of formerly parasitic elements and a different explanation must be provided.
5) Provide a specific explanation for how the great majority of transposable elements in the human genome can be functional while showing clear signs of being inactive. Most TEs in the human genome have experienced mutations in regions that render them incapable of undergoing transposition. Many are so degraded by mutation as to be hardly recognizable. How these highly mutated elements carry out a specific function needs to be explained.
6) Provide an explanation for why the DNA sequences of non-coding regions in different species appear to correspond to degree of relatedness. If species do not share common ancestors, then an alternate explanation is required for why species that are claimed to be close relatives exhibit similar sequences whereas those that are claimed to be more distant relatives possess DNA sequences that are not as similar.
7) Propose a testable explanation for why similar species may have widely different quantities of non-coding DNA in their genomes. A simple example is provided by onions and members of the same genus.
8) If one does accept common descent, propose a testable explanation for how there can be significant reductions in DNA content in some lineages. There is evidence that many lineages have experienced losses of non-coding DNA. For example, the evolution of saurischian dinosaurs appears to have included a reduction in DNA amount. How this loss of DNA could occur requires explanation under the assumption that all non-coding DNA in the ancestor’s genome was functional.
More could be added to such a list, but I suspect that this will be enough to provide ID proponents with a prime opportunity to demonstrate their scientific credibility.
So, I have recently become aware that Genomicron is cited on an intelligent design wiki entry for “junk DNA“. They quote two paragraphs from my post A word about “junk DNA”. Specifically, a paragraph in which I critique the term “junk DNA” as unnecessarily implying non-function for all non-coding DNA, and a paragraph in which I list many (unsubstantiated) hypotheses about universal functions for non-coding DNA. Here are two paragraphs from the post that they don’t quote:
To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions). Case in point: a few years ago, much ado was made of Beaton and Cavalier-Smith’s (1999) titular proclamation, based on a survey of cryptomonad nuclear and nucleomorphic genomes, that “eukaryotic non-coding DNA is functionalâ€. The point was evidently lost that the function proposed by Beaton and Cavalier-Smith (1999) was based entirely on coevolutionary interactions between nucleus size and cell size.
Here’s a quote they are welcome to use: Simply saying “junk DNA will turn out to have a function” is not a scientifically actionable prediction unless you specify what that function will be and a way to test the proposed function.
I have some quick questions for the scientists, journalists, and neither-nors who read Genomicron. Should scientists nit-pick inaccuracies in news reports? Does it do any good to keep journalism on track, or is it a waste of time (or maybe even irritating)? What else can we do to improve the accuracy of science reporting, in particular involving cooperation with rather than criticism of science writers? Since I don’t have the answers yet, I will just go ahead with a snarky post in the meantime.
Here is what triggered this query. I was reading this story, How Neutral Genetic Drift Shaped Our Genome, at Scientific Blogging (based on a Johns Hopkins press office release), when I came upon this gem:
When they expanded their study across the whole human genome, they found more than 1200 such pieces of mitochondrial DNA of various lengths [nuclear pseudogenes of mitochondrial origin, or numts] embedded into chromosomes. While chimps have a comparable number, mice and rats only have around 600 numts. Since they increase in frequency as species advance, it suggested there was some evolutionary purpose to keeping them around.
Strikingly, however, none of these numts contained the blueprint (an actual gene) to make a protein that does anything, nor did they seem to control the function of any nearby genes. “At best, it seems numts are a neutral part of our genome,†says Katsanis. “If anything, they may be mildly negative since long repeat sequences can be unstable or get inserted inside genes and disrupt them.â€
Ok, the nit-picker in me really wants to point out that evolution is not a process under which “species advance”, that there is no such thing as an “evolutionary purpose”, that genes are not blueprints, that this study deals with a tiny fraction of the genome, that the idea that “they accumulate steadily” makes no sense in terms of either function or neutrality given what they just said about rodents versus primates, and that of course these pseudogenes — of mitochondrial descent, no less — do not encode a functional protein by definition. There is absolutely nothing surprising in the observation that they evolve neutrally in the nuclear genome.
To Larry Moran’s recent post Stop the Press!!! … Genes Have Regulatory Sequences!, we can add Pseudogenes do not encode functional proteins! Next: DNA includes both protein-coding genes and non-coding sequence!
(Update: Scientific Blogging redeems itself with a good post about the ENCODE hype here) (Another update: Evolution Diary uncritically posts the same nonsensical press release here.) (Another update: The paper itself is actually far more interesting than this poorly crafted press release would make it appear. See the open access pdf here.)
The latest edition of the blog carnival Mendel’s Garden is now up at Eye on DNA. It includes one article from Genomicron, plus lots of other genetic goodies. Thanks also to Hsien-Hsien Lei for posting it today rather than last week so that it would not compete with Gene Genie here at Genomicron.
I used to subscribe to (and quite enjoy) The Scientist when it was a free publication, but have mostly stopped reading it now. Two stories in the latest issue were pointed out to me by readers of Genomicron, so I thought I should provide some brief comments.
The first relates to an editorial by Richard Gallagher entitled “Junk Worth Keeping“, which asks “Is it time to retire provocative descriptors such as ‘junk DNA’?”. The answer, says Gallagher, is “no”. Why? Because “junk DNA” is useful for… framing. He cites Nisbet, although as I have come to learn, framing, sensu Mooney and Nisbet, applies to conveying science in a particular way to help win an election. I’m not sure what “junk DNA” has to do with defeating the Republicans as per Mooney’s formulation of framing, and in any case, Greg Laden has already provided a very useful discussion of the fact that “junk DNA” is a frame that anti-evolutionists exploit because it allows them to obfuscate genetic knowledge to their own ends. They do, of course, get both the history and the science of the term totally wrong, but that’s not the point when it comes to spin. In other words, the term “junk DNA” is a horrible way to communicate the complexity of non-coding DNA to an audience with no background in evolution or genome biology. Granted, it does get them to talk about the issue, but I believe there must be better ways to do this than to set up the discussion to be oversimplified and confused. [Hat tip: junkdna.com]
The second comes from a story by Melissa Lee Phillips reporting “Surprises in the Sea Anemone Genome“. Here are some statements of interest:
“…the sea anemone, one of the oldest living animal species on Earth…”
“The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution.”
“It’s surprising to find such a ‘high level of genomic complexity in a supposedly primitive animal such as the sea anemone,’ Koonin told The Scientist.”
I will probably do an entire post on the common fallacy of describing one extant lineage as older than another (common descent dictates that all contemporary lineages are of exactly the same age, although some have undergone more branching and/or morphological change than others). But statement #1 is especially inaccurate because the age of a species is not the same thing as the age of a lineage (which is what the author meant to describe). This species (Nematostella vectensis) could, for all we know, be very young, and certainly there is no basis in evidence for calling it one of the oldest species on Earth. (The original paper in Science is at least clearer on this, describing the Cnidaria as “the oldest eumetazoan phylum”, though this is difficult to substantiate given that no unambiguous fossils exist for eumetazoa prior to the Cambrian, at which time early representatives of modern phyla were already present; they cite two papers that can, at best, only suggest that Cnidarians [and perhaps molluscs] were present among the Ediacaran biota). And, of course, “the” sea anemone is a misnomer as this name applies to the entire order Actinaria, within which there are several dozen families.
Statement #2 may refer to a widely held belief among the public (and perhaps among some genome sequencers), but the expectation that complexity always increases in evolution is a fallacy that was abandoned long ago by evolutionary biologists. (It also bears noting that organisms do not evolve, populations do). A huge amount of the diversity on this planet is composed of parasites, and their evolution often involves simplification. In this case, it is not morphological but genome evolution that is under discussion, and there is really no reason to expect an increase in complexity here either. Gene loss is a well known phenomenon, and in fact one could make a case that streamlining of the genome or having one gene do multiple things is related to increased morphological complexity whereas gene number is not. Take, for example, the sea urchin, whose immune system seams to involve a large number of genes, as compared to a vertebrate, whose immune system generates nearly endless variation by recombining a comparatively limited number of genes. (Incidentally, the anemone genome appears to contain 18,000 genes). Statement #3 is not necessarily inaccurate, but I caution readers that it must be interpreted in a certain way. “Primitive” does not mean “less complex” or “less advanced”, it means “more like the last common ancestor of the groups being compared”. In this sense, a sea anemone is probably more like the last common ancestor of all animals than is, say, a fly. But this is also a modern species whose overall lineage has been around for exactly the same amount of time as that of the fly. The anemone lineage may have undergone fewer morphological changes (though still probably a lot) than the lineage that led to insects, but the anemone itself is not the common ancestor and in fact may bear only a modest resemblance to the ancestor. This is exactly the same confusion people face when thinking about humans and chimpanzees. Chimps were not the ancestor of humans, and may bear only a modest resemblance to the common ancestor of the two lineages — the two split millions of years ago, and both lineages have undergone considerable change since, with many species arising and disappearing in the meantime.
I like to see these interesting topics covered in The Scientist, but I must admit that these two pieces in particular do not inspire me to re-subscribe to the magazine.
While I’m at it, let me register a small complaint about the story by Elizabeth Pennisi in Science [Sea Anemone Provides a New View of Animal Evolution]. I have become mostly resigned to the fact that science writers will insist on describing genome sequencing as “decoding” a genome, and this story is no exception. What bothers me more is that Pennisi is so sloppy in characterizing evolution as a “progressive” process. Thus, she argues that “genome sequencers have just jumped down to a lower branch on the tree of life“, and that “until now, researchers have relied heavily on the sequenced genomes of the fruit fly, nematode, and that of a few other invertebrates to understand genome evolution leading up to the vertebrates“. (Update: Apparently the authors the paper cautioned Pennisi about this, but to no avail!).
Evidently, we have a lot of work to do in clearing up the basic details of how evolution occurs.
Readers of this blog will be aware that I am experimenting with blogging as a mechanism of public outreach in science. This time, I want to try a different experiment. Specifically, I want to see how much good can come from a single blog post.
Here is the story. In November, 2006, my father fulfilled a lifelong dream of traveling to Africa to explore the cradle of humanity and to experience first-hand the cultural and zoological diversity to which the continent is home. Amidst the beauty of the landscape and the hospitality of the people, he was struck — as I am sure anyone who visits Africa must be — by the tragedy of poverty and disease (especially malaria and AIDS) juxtaposed with a tangible sense of happiness and hope.
My father has spent most of his life helping others. A social worker by training, he has dedicated much of his career to protecting the rights and dignity of the mentally challenged. This has included efforts to move as many people as possible out of (often horrific) institutions and into dignified group home environments. He has also developed programs to assist individuals with mental difficulties in returning to post-secondary education, and most recently has worked to train a new generation of social work students. In light of this, it comes as little surprise to me that he felt compelled to help the people he befriended in Africa.
My stepmother is equally generous. In her capacity as a gifted singer, musician, and teacher, she has devoted herself over the past decade to creating community choirs for both children and adults in the small town in which they live. The effects that this has had on the confidence and sense of community of the participants is remarkable.
The next phase in their lives will involve the most ambitious endeavour that either has attempted. In six months, they will be selling their house, resigning from their current jobs, and moving to Livingstone, Zambia.
While there, they will work to revamp the local Victoria Hall and to create a musical theatre program showcasing the traditional song and dance of Zambia. This is intended to capitalize on the rapidly growing tourism industry in the Livingstone area (which is less than 10km from Victoria Falls) and will provide a self-sustaining source of income for local performers and tradespeople. It will also be used to inject funds into the Livingstone economy and to improve the desperate conditions of the local hospital and schools.
The Victoria Hall in Livingstone, Zambia.
The mission statement of the project is described as follows:
Mission Statement:
The Livingstone Performing Arts Foundation (LiPAF) mission is to create and perform traditional and original works of music, song and dance which reflect the history, culture, languages and ethnic background of Zambia. Operating as a not for profit organization, LiPAF will enrich the community by providing opportunities for employment, sponsorship of a variety of needy programs and services, and educational programs on topics related to the human condition.
Objectives of the Project:
To operate a not-for-profit Foundation.
To promote the rich cultural diversity existing in Zambia and the Kavango-Zambezi region.
To promote the city of Livingstone, the country of Zambia, and the region of Kavango-Zambezi, as a tourist destination.
To provide employment for local residents.
To raise funds for the sponsorship of various community projects
To assist in the promotion and expansion of the service related industry (restaurants, merchants, etc.).
To cooperate with other community-based groups within the Livingstone district.
To improve and enhance the educational aspect of the city library.
To provide music programs in local schools.
Plans for the redesigned Victoria Hall.
I should emphasize that this is an independent, non-profit project. It is not being carried out with any expectation of personal reward (in this life or any other). It is simply an attempt by two phenomenal people to make a difference by applying their talents to benefit others in need.
So far, they have been hard at work coordinating with local and federal governments in Zambia and generating funds to pay for the project through fund raising events and by making countless presentations to local service clubs and other organizations. They have been tireless in these efforts, but of course they cannot do it alone.
The question I posed as the title of this post is “How much good can one blog post do?”. I am hopeful that the answer will be a resounding “A great deal!”. There are many ways to help.
Maybe you can inform your colleagues, friends, and family members about this post and the foundation website.
Maybe you are a teacher and your school is throwing out old textbooks, dictionaries, or atlases that could be given to the local elementary/high school.
Maybe you can help to provide the school with other necessities such as science equipment. I am planning to visit and to teach some basic biology classes, but the school barely has desks, let alone microscopes.
Maybe you work in the performing arts industry and can help with the acquisition of sound or lighting equipment.
Maybe you’re an artist and could donate some of your work to be used in a fund raising auction.
Maybe you work for a charity, shipping company, or other organization that would be interested in assisting the program logistically or financially.
And of course, you can make a personal donation in any sum. I have set up a PayPal account for them to receive donations. The donation is not tax-deductible as the foundation is registered as a not-for-profit organization in Zambia, but 100% of it will be put to use in support of the project. See also their 100 from 500 Club, in which there is a chance to win some great prizes donated by artist friends.
The motto that they have adopted, a quote from Margaret Mead, is “Never doubt that a small group of thoughtful committed citizens can change the world. Indeed, it is the only thing that ever has.”
I will miss my parents when they go, but I can do no other but admire and support their decision to do so.
__________
It took some doing, but I have been able to format the video presentation that they have been giving to local organizations for posting here. It’s meant to be shown on a projection screen, but I think the text is legible even at this size. This really sets the stage for what they are trying to do, and has a very positive message overall with an emphasis on the beauty of Zambia.
Thank you to everyone who has contributed already — every little bit helps!
To find out more, please visit the Livingstone Performing Arts Foundation website and blog.
Many science blogs have a regular series on particular subjects. Thus far I have not done anything like that, but I think the “X vs. Y” pieces could make for a useful series. I shall dub it “Concept contrasts”, and present the first three in the following compendium.
